Multiple sequence alignment - TraesCS7A01G176100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G176100 chr7A 100.000 3676 0 0 1 3676 129062069 129058394 0.000000e+00 6789
1 TraesCS7A01G176100 chr7A 97.091 928 27 0 1 928 641708516 641709443 0.000000e+00 1565
2 TraesCS7A01G176100 chr7A 96.778 931 28 2 1 929 171262180 171263110 0.000000e+00 1552
3 TraesCS7A01G176100 chr7B 91.000 2089 108 23 929 2977 91296424 91294376 0.000000e+00 2743
4 TraesCS7A01G176100 chr7B 91.011 1869 94 19 1857 3676 91292719 91290876 0.000000e+00 2453
5 TraesCS7A01G176100 chr7D 90.310 2095 125 28 927 2977 129975224 129973164 0.000000e+00 2673
6 TraesCS7A01G176100 chr1A 97.300 926 24 1 2 926 65828873 65829798 0.000000e+00 1570
7 TraesCS7A01G176100 chr1A 81.731 624 73 23 1253 1870 167214869 167214281 1.990000e-132 483
8 TraesCS7A01G176100 chr1A 91.613 310 25 1 2419 2728 167153726 167153418 9.430000e-116 427
9 TraesCS7A01G176100 chr5A 96.764 927 29 1 1 927 663785099 663786024 0.000000e+00 1544
10 TraesCS7A01G176100 chr5A 96.636 862 28 1 67 928 527627766 527626906 0.000000e+00 1430
11 TraesCS7A01G176100 chr6A 96.245 932 34 1 1 931 534670764 534671695 0.000000e+00 1526
12 TraesCS7A01G176100 chr3A 96.013 928 33 3 1 927 99306512 99305588 0.000000e+00 1506
13 TraesCS7A01G176100 chr3A 96.429 504 18 0 425 928 580636620 580636117 0.000000e+00 832
14 TraesCS7A01G176100 chr4A 95.366 928 22 1 1 928 319839375 319838469 0.000000e+00 1456
15 TraesCS7A01G176100 chr2A 95.254 590 28 0 1 590 710378053 710377464 0.000000e+00 935
16 TraesCS7A01G176100 chr1B 84.586 532 63 10 1343 1870 211629644 211630160 9.110000e-141 510
17 TraesCS7A01G176100 chr1B 92.025 326 25 1 2417 2742 210207842 210208166 1.200000e-124 457
18 TraesCS7A01G176100 chr1B 80.367 545 82 13 1890 2412 210145373 210145914 1.240000e-104 390
19 TraesCS7A01G176100 chr1D 91.509 212 17 1 2412 2623 136947933 136948143 1.290000e-74 291
20 TraesCS7A01G176100 chr1D 83.186 339 34 9 2096 2412 136946827 136947164 4.640000e-74 289
21 TraesCS7A01G176100 chr1D 84.685 222 25 4 2760 2977 136950026 136950242 2.880000e-51 213
22 TraesCS7A01G176100 chr1D 92.308 130 9 1 2613 2742 136949721 136949849 2.250000e-42 183


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G176100 chr7A 129058394 129062069 3675 True 6789 6789 100.0000 1 3676 1 chr7A.!!$R1 3675
1 TraesCS7A01G176100 chr7A 641708516 641709443 927 False 1565 1565 97.0910 1 928 1 chr7A.!!$F2 927
2 TraesCS7A01G176100 chr7A 171262180 171263110 930 False 1552 1552 96.7780 1 929 1 chr7A.!!$F1 928
3 TraesCS7A01G176100 chr7B 91290876 91296424 5548 True 2598 2743 91.0055 929 3676 2 chr7B.!!$R1 2747
4 TraesCS7A01G176100 chr7D 129973164 129975224 2060 True 2673 2673 90.3100 927 2977 1 chr7D.!!$R1 2050
5 TraesCS7A01G176100 chr1A 65828873 65829798 925 False 1570 1570 97.3000 2 926 1 chr1A.!!$F1 924
6 TraesCS7A01G176100 chr1A 167214281 167214869 588 True 483 483 81.7310 1253 1870 1 chr1A.!!$R2 617
7 TraesCS7A01G176100 chr5A 663785099 663786024 925 False 1544 1544 96.7640 1 927 1 chr5A.!!$F1 926
8 TraesCS7A01G176100 chr5A 527626906 527627766 860 True 1430 1430 96.6360 67 928 1 chr5A.!!$R1 861
9 TraesCS7A01G176100 chr6A 534670764 534671695 931 False 1526 1526 96.2450 1 931 1 chr6A.!!$F1 930
10 TraesCS7A01G176100 chr3A 99305588 99306512 924 True 1506 1506 96.0130 1 927 1 chr3A.!!$R1 926
11 TraesCS7A01G176100 chr3A 580636117 580636620 503 True 832 832 96.4290 425 928 1 chr3A.!!$R2 503
12 TraesCS7A01G176100 chr4A 319838469 319839375 906 True 1456 1456 95.3660 1 928 1 chr4A.!!$R1 927
13 TraesCS7A01G176100 chr2A 710377464 710378053 589 True 935 935 95.2540 1 590 1 chr2A.!!$R1 589
14 TraesCS7A01G176100 chr1B 211629644 211630160 516 False 510 510 84.5860 1343 1870 1 chr1B.!!$F3 527
15 TraesCS7A01G176100 chr1B 210145373 210145914 541 False 390 390 80.3670 1890 2412 1 chr1B.!!$F1 522
16 TraesCS7A01G176100 chr1D 136946827 136950242 3415 False 244 291 87.9220 2096 2977 4 chr1D.!!$F1 881

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
257 258 0.832983 TTGTAGGCTGTGTACGGGGT 60.833 55.0 0.00 0.0 0.00 4.95 F
1554 1565 0.179073 ACCGCAGATATGTCAGGTGC 60.179 55.0 4.03 0.0 31.01 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2225 1.000955 TCACTCCCTGTCGAAGAAAGC 59.999 52.381 0.00 0.00 41.48 3.51 R
3262 8530 0.388294 CTGCTCGATCCAGCTGATGA 59.612 55.000 17.39 5.01 39.97 2.92 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.818674 GGGGCAAACTACAAGTGGATG 59.181 52.381 0.00 0.00 0.00 3.51
65 66 4.886579 AGTGGATGTGGAAAGCAAAAATC 58.113 39.130 0.00 0.00 0.00 2.17
253 254 2.481449 GGAGGATTGTAGGCTGTGTACG 60.481 54.545 0.00 0.00 0.00 3.67
257 258 0.832983 TTGTAGGCTGTGTACGGGGT 60.833 55.000 0.00 0.00 0.00 4.95
454 456 7.422399 GTTTACTCTGCATGTGGTTTTCTTAA 58.578 34.615 0.00 0.00 0.00 1.85
714 718 6.256643 AGTAACCCTCCTAAAACTTGTTGA 57.743 37.500 0.00 0.00 0.00 3.18
761 765 1.489649 TGGTTTTAGGGTGTCGTTGGA 59.510 47.619 0.00 0.00 0.00 3.53
811 815 1.608590 CGAGTGCTCATTGTGGGTTTT 59.391 47.619 0.00 0.00 0.00 2.43
838 842 1.376553 GCTTTGAGCTCGCTTCCCT 60.377 57.895 9.64 0.00 38.45 4.20
846 850 2.166664 GAGCTCGCTTCCCTTTTCTAGA 59.833 50.000 0.00 0.00 0.00 2.43
963 967 9.594478 AGTTCATCAAAAGTAAAACCGAAAAAT 57.406 25.926 0.00 0.00 0.00 1.82
982 990 5.369409 AAATAGCCCCAAACTACTAGGTC 57.631 43.478 0.00 0.00 0.00 3.85
997 1005 0.976590 AGGTCTCCGCTAACCTTCCC 60.977 60.000 0.00 0.00 43.45 3.97
1072 1080 4.196965 CGCCCCTTCGGACTAAAC 57.803 61.111 0.00 0.00 0.00 2.01
1162 1170 1.219393 CGGTGAGCTCCCTTTCTCC 59.781 63.158 12.15 1.78 0.00 3.71
1196 1204 1.935873 CACGCGATTCATGGATCTGTT 59.064 47.619 15.93 0.00 0.00 3.16
1197 1205 1.935873 ACGCGATTCATGGATCTGTTG 59.064 47.619 15.93 1.91 0.00 3.33
1198 1206 1.935873 CGCGATTCATGGATCTGTTGT 59.064 47.619 12.27 0.00 0.00 3.32
1209 1217 1.672881 GATCTGTTGTGGCCAGTATGC 59.327 52.381 5.11 0.00 31.97 3.14
1217 1225 2.040278 TGTGGCCAGTATGCTTCTCTTT 59.960 45.455 5.11 0.00 31.97 2.52
1266 1276 7.391833 AGAAACTCCACCTTCATAAAATCAGTC 59.608 37.037 0.00 0.00 0.00 3.51
1267 1277 5.501156 ACTCCACCTTCATAAAATCAGTCC 58.499 41.667 0.00 0.00 0.00 3.85
1321 1331 4.694760 TCTGTGCTTGGTATCTGCATAT 57.305 40.909 0.00 0.00 39.00 1.78
1430 1441 5.582269 ACATTCGACTATCCATGTGAGTTTG 59.418 40.000 0.00 0.00 0.00 2.93
1444 1455 5.116180 TGTGAGTTTGTTCGATTCACTCTT 58.884 37.500 12.90 0.00 39.05 2.85
1457 1468 6.699204 TCGATTCACTCTTCTGCTAATCATTC 59.301 38.462 0.00 0.00 0.00 2.67
1466 1477 9.727627 CTCTTCTGCTAATCATTCCATTTTTAC 57.272 33.333 0.00 0.00 0.00 2.01
1506 1517 5.458041 AATTCTTGACCCATGTTCACTTG 57.542 39.130 0.00 0.00 0.00 3.16
1515 1526 3.057315 CCCATGTTCACTTGATGGTTGAC 60.057 47.826 0.00 0.00 35.75 3.18
1537 1548 5.219633 ACGAATTAATCAAGCAACAACACC 58.780 37.500 0.00 0.00 0.00 4.16
1549 1560 2.741517 CAACAACACCGCAGATATGTCA 59.258 45.455 0.00 0.00 0.00 3.58
1554 1565 0.179073 ACCGCAGATATGTCAGGTGC 60.179 55.000 4.03 0.00 31.01 5.01
1597 1608 1.733399 GGACAAGCTCGTCGACCAC 60.733 63.158 10.58 0.00 36.73 4.16
1616 1627 1.349026 ACCATCTCAGTGTGGTGAAGG 59.651 52.381 7.03 3.24 46.55 3.46
1687 1698 5.293569 GTCTATGGGTTCGAGGTAACATTTG 59.706 44.000 0.00 0.00 41.41 2.32
1726 1737 2.823984 TGCTTGTGCATCTTTTTGGTG 58.176 42.857 0.00 0.00 45.31 4.17
1728 1739 3.197265 GCTTGTGCATCTTTTTGGTGTT 58.803 40.909 0.00 0.00 39.41 3.32
1729 1740 3.001533 GCTTGTGCATCTTTTTGGTGTTG 59.998 43.478 0.00 0.00 39.41 3.33
1753 1764 7.720442 TGTGTTATATGATCTGACTTCTGAGG 58.280 38.462 0.00 0.00 0.00 3.86
1801 1818 1.821332 GGTCAGCTGCATGGTAGCC 60.821 63.158 9.47 0.00 42.07 3.93
1850 1867 7.845340 GCAGTCATTTGCTTGGGTTATCCAC 62.845 48.000 0.00 0.00 39.73 4.02
1898 1923 5.705905 GTGTACTTAGATTTGGGTTGCTTCT 59.294 40.000 0.00 0.00 0.00 2.85
1902 1927 3.243359 AGATTTGGGTTGCTTCTTGGA 57.757 42.857 0.00 0.00 0.00 3.53
1913 1938 2.224378 TGCTTCTTGGACTGTCTCCTTG 60.224 50.000 7.85 0.00 40.26 3.61
1935 1960 4.158579 TGTTGAATTGTTGTGCCTGTGTTA 59.841 37.500 0.00 0.00 0.00 2.41
1968 2001 5.410132 TCAACTATAACACACACCGAAATGG 59.590 40.000 0.00 0.00 46.41 3.16
1972 2005 7.332557 ACTATAACACACACCGAAATGGATTA 58.667 34.615 0.00 0.00 42.00 1.75
1999 2032 7.650903 GGATCTCCATCAGAATTTAATTGTTGC 59.349 37.037 0.00 0.00 33.62 4.17
2021 2054 4.567959 GCAGAATTCAACCATTTATGCACC 59.432 41.667 8.44 0.00 32.97 5.01
2022 2055 5.625197 GCAGAATTCAACCATTTATGCACCT 60.625 40.000 8.44 0.00 32.97 4.00
2024 2057 7.685155 GCAGAATTCAACCATTTATGCACCTAT 60.685 37.037 8.44 0.00 32.97 2.57
2089 2122 3.961480 TGCTACAACTATGCAGTGACT 57.039 42.857 0.00 0.00 34.36 3.41
2091 2124 4.245660 TGCTACAACTATGCAGTGACTTC 58.754 43.478 0.00 0.00 34.36 3.01
2179 2215 7.170393 ACTAAAGAAGCTGTTCCTTTTGTTT 57.830 32.000 8.34 0.00 32.48 2.83
2180 2216 7.611770 ACTAAAGAAGCTGTTCCTTTTGTTTT 58.388 30.769 8.34 0.00 32.48 2.43
2181 2217 6.726258 AAAGAAGCTGTTCCTTTTGTTTTG 57.274 33.333 0.00 0.00 32.48 2.44
2182 2218 4.183865 AGAAGCTGTTCCTTTTGTTTTGC 58.816 39.130 0.00 0.00 32.48 3.68
2183 2219 3.608316 AGCTGTTCCTTTTGTTTTGCA 57.392 38.095 0.00 0.00 0.00 4.08
2184 2220 4.141233 AGCTGTTCCTTTTGTTTTGCAT 57.859 36.364 0.00 0.00 0.00 3.96
2185 2221 4.122046 AGCTGTTCCTTTTGTTTTGCATC 58.878 39.130 0.00 0.00 0.00 3.91
2186 2222 4.122046 GCTGTTCCTTTTGTTTTGCATCT 58.878 39.130 0.00 0.00 0.00 2.90
2187 2223 4.571984 GCTGTTCCTTTTGTTTTGCATCTT 59.428 37.500 0.00 0.00 0.00 2.40
2188 2224 5.065090 GCTGTTCCTTTTGTTTTGCATCTTT 59.935 36.000 0.00 0.00 0.00 2.52
2189 2225 6.419980 TGTTCCTTTTGTTTTGCATCTTTG 57.580 33.333 0.00 0.00 0.00 2.77
2238 2287 3.491639 CACCGAGAGACGAGATACTACTG 59.508 52.174 0.00 0.00 45.77 2.74
2327 2408 9.114952 GTGAAAATTTTAGGGATTGTTTGGAAA 57.885 29.630 2.75 0.00 0.00 3.13
2332 2413 5.659440 TTAGGGATTGTTTGGAAAGCATC 57.341 39.130 0.00 0.00 36.76 3.91
2415 3269 6.711645 GTGTTCCAAACAGGGTGTAAATAGTA 59.288 38.462 0.00 0.00 43.10 1.82
2442 3296 0.804989 GAATCTTGACTTGCGGTGGG 59.195 55.000 0.00 0.00 0.00 4.61
2585 3439 5.925969 AGTCAGCCAAAAATACCAAAAATCG 59.074 36.000 0.00 0.00 0.00 3.34
2608 3462 4.498682 GGCTGGAATAAGTCAACATGATGC 60.499 45.833 0.00 0.00 0.00 3.91
2686 5128 2.930682 GCTTAACCTAGCTGTTCCTTCG 59.069 50.000 0.00 0.00 38.15 3.79
2765 5210 3.435275 AGGGGAAAGATTCTGGCTTTTC 58.565 45.455 0.00 0.00 35.83 2.29
2770 5215 5.173664 GGAAAGATTCTGGCTTTTCAATGG 58.826 41.667 0.00 0.00 35.83 3.16
2780 5225 7.118723 TCTGGCTTTTCAATGGTCTAATATGT 58.881 34.615 0.00 0.00 0.00 2.29
2781 5226 7.067372 TCTGGCTTTTCAATGGTCTAATATGTG 59.933 37.037 0.00 0.00 0.00 3.21
2907 8151 3.438017 TTTTGCCTTGCACCGTGCC 62.438 57.895 20.67 5.83 44.23 5.01
2923 8172 3.191162 CCGTGCCTTTTCATGATTGAGAA 59.809 43.478 0.00 0.00 32.27 2.87
2977 8226 6.762333 TGCTCTTGCTGCTTATCTATGAATA 58.238 36.000 0.00 0.00 40.48 1.75
2999 8264 5.957771 ATATCAGTGGCAAGTTTCCTCTA 57.042 39.130 0.00 0.00 0.00 2.43
3000 8265 4.851639 ATCAGTGGCAAGTTTCCTCTAT 57.148 40.909 0.00 0.00 0.00 1.98
3006 8271 4.034510 GTGGCAAGTTTCCTCTATGAATCG 59.965 45.833 0.00 0.00 0.00 3.34
3063 8331 8.792830 TTTCTTAGAAAGGATCAGTACAATGG 57.207 34.615 2.94 0.00 0.00 3.16
3109 8377 6.966021 TGTATTTGCAAAAGGAGTAACAGAC 58.034 36.000 17.19 0.00 0.00 3.51
3126 8394 1.361668 GACGTGCCAGTACCATGCAG 61.362 60.000 0.00 1.05 35.33 4.41
3133 8401 2.372264 CCAGTACCATGCAGATTGCTT 58.628 47.619 2.48 0.00 45.31 3.91
3147 8415 6.203530 TGCAGATTGCTTAATTCCTCTTATCG 59.796 38.462 2.48 0.00 45.31 2.92
3188 8456 4.660789 ACCATGCATCTTGCTTAATTCC 57.339 40.909 0.00 0.00 45.31 3.01
3196 8464 5.435291 CATCTTGCTTAATTCCTCTGTCCT 58.565 41.667 0.00 0.00 0.00 3.85
3213 8481 0.541863 CCTGGCAATTAGGACCGTCT 59.458 55.000 0.00 0.00 37.52 4.18
3214 8482 1.065418 CCTGGCAATTAGGACCGTCTT 60.065 52.381 0.00 0.00 37.52 3.01
3216 8484 2.678336 CTGGCAATTAGGACCGTCTTTC 59.322 50.000 0.00 0.00 0.00 2.62
3218 8486 2.613691 GCAATTAGGACCGTCTTTCGA 58.386 47.619 0.00 0.00 42.86 3.71
3220 8488 3.001330 GCAATTAGGACCGTCTTTCGATG 59.999 47.826 0.00 0.00 42.86 3.84
3221 8489 4.181578 CAATTAGGACCGTCTTTCGATGT 58.818 43.478 0.00 0.00 42.86 3.06
3235 8503 8.567221 CGTCTTTCGATGTATTTTGACAAAATC 58.433 33.333 25.53 17.97 40.56 2.17
3251 8519 5.079643 ACAAAATCATCCTTTACTGTGGCT 58.920 37.500 0.00 0.00 0.00 4.75
3262 8530 0.823356 ACTGTGGCTTTCCGTTGCAT 60.823 50.000 0.00 0.00 34.14 3.96
3308 8576 6.765989 AGCAACTACTGTTCAAGAATGTACAA 59.234 34.615 0.00 0.00 36.56 2.41
3354 8622 4.980434 GCATAAATTAGGCAGCACAGAATG 59.020 41.667 4.66 0.00 37.53 2.67
3356 8624 6.681120 GCATAAATTAGGCAGCACAGAATGAA 60.681 38.462 4.66 0.00 35.77 2.57
3357 8625 4.978083 AATTAGGCAGCACAGAATGAAG 57.022 40.909 0.00 0.00 39.69 3.02
3358 8626 3.423539 TTAGGCAGCACAGAATGAAGT 57.576 42.857 0.00 0.00 39.69 3.01
3359 8627 2.283145 AGGCAGCACAGAATGAAGTT 57.717 45.000 0.00 0.00 39.69 2.66
3361 8629 3.077359 AGGCAGCACAGAATGAAGTTAC 58.923 45.455 0.00 0.00 39.69 2.50
3416 8684 2.486203 TGACATTACCGGCAATGAACAC 59.514 45.455 30.01 18.21 38.01 3.32
3423 8691 0.457166 CGGCAATGAACACATGCAGG 60.457 55.000 0.00 0.00 0.00 4.85
3427 8695 1.542472 CAATGAACACATGCAGGCTGA 59.458 47.619 20.86 3.68 0.00 4.26
3476 8744 0.656259 TCGATCCTAGCAGTTCGTCG 59.344 55.000 0.00 0.00 33.52 5.12
3481 8749 1.941294 TCCTAGCAGTTCGTCGAGATC 59.059 52.381 0.00 0.00 0.00 2.75
3497 8765 2.746362 GAGATCGAAATCATCCATGCCC 59.254 50.000 0.00 0.00 34.07 5.36
3534 8802 6.847400 TGAAGAACAGAAACATGAAACGAAA 58.153 32.000 0.00 0.00 0.00 3.46
3594 8864 5.607939 TGATAGTAAAGAAAGGGCGATCA 57.392 39.130 0.00 0.00 0.00 2.92
3609 8879 1.722034 GATCAGTGCTCCTCCCCATA 58.278 55.000 0.00 0.00 0.00 2.74
3623 8893 3.461831 CTCCCCATATTTCACCCACCTTA 59.538 47.826 0.00 0.00 0.00 2.69
3643 8913 3.791973 AGACATGAACTGATCGAGGTC 57.208 47.619 0.00 3.95 39.12 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.977854 AGGGGGATTTTTGCTTTCCAC 59.022 47.619 0.00 0.00 31.83 4.02
65 66 8.575589 CAAAGGAAAATTTGAATTTTAAGGGGG 58.424 33.333 12.87 1.50 45.70 5.40
238 239 0.832983 ACCCCGTACACAGCCTACAA 60.833 55.000 0.00 0.00 0.00 2.41
253 254 0.974010 TGGACACAGATCCGTACCCC 60.974 60.000 0.00 0.00 42.24 4.95
257 258 3.827876 TGTTACTTGGACACAGATCCGTA 59.172 43.478 0.00 0.00 42.24 4.02
454 456 1.985159 TCATCAAACCTGCCCAGTAGT 59.015 47.619 0.00 0.00 0.00 2.73
714 718 6.351117 CCGACTAACTCTAACCAGGAGAATTT 60.351 42.308 0.00 0.00 35.10 1.82
761 765 1.322538 GCTCACCATGGGGCGAAAAT 61.323 55.000 18.09 0.00 37.90 1.82
811 815 2.669569 GCTCAAAGCACCGCTGGA 60.670 61.111 1.50 0.00 41.89 3.86
881 885 6.126409 CCCCTTTCCATTACTTAGCATAACA 58.874 40.000 0.00 0.00 0.00 2.41
955 959 4.014406 AGTAGTTTGGGGCTATTTTTCGG 58.986 43.478 0.00 0.00 0.00 4.30
963 967 3.629282 GGAGACCTAGTAGTTTGGGGCTA 60.629 52.174 0.00 0.00 37.32 3.93
982 990 1.345715 ATGGGGGAAGGTTAGCGGAG 61.346 60.000 0.00 0.00 0.00 4.63
1196 1204 1.279496 AGAGAAGCATACTGGCCACA 58.721 50.000 0.00 0.00 0.00 4.17
1197 1205 2.409948 AAGAGAAGCATACTGGCCAC 57.590 50.000 0.00 0.00 0.00 5.01
1198 1206 2.618816 CCAAAGAGAAGCATACTGGCCA 60.619 50.000 4.71 4.71 0.00 5.36
1209 1217 3.282885 GGGGCATTCTACCAAAGAGAAG 58.717 50.000 0.00 0.00 36.41 2.85
1217 1225 1.484038 GCAAATGGGGCATTCTACCA 58.516 50.000 0.00 0.00 38.88 3.25
1332 1342 7.719193 TGGAAGAATCAATTGTCTTGTCAGTTA 59.281 33.333 14.21 0.00 34.23 2.24
1341 1352 4.015084 CCAGCTGGAAGAATCAATTGTCT 58.985 43.478 29.88 0.00 37.39 3.41
1342 1353 4.012374 TCCAGCTGGAAGAATCAATTGTC 58.988 43.478 33.41 0.00 42.18 3.18
1343 1354 4.038271 TCCAGCTGGAAGAATCAATTGT 57.962 40.909 33.41 0.00 42.18 2.71
1430 1441 5.807520 TGATTAGCAGAAGAGTGAATCGAAC 59.192 40.000 0.00 0.00 0.00 3.95
1444 1455 6.039270 CGGGTAAAAATGGAATGATTAGCAGA 59.961 38.462 0.00 0.00 31.31 4.26
1466 1477 3.629142 ATTAAGAACTGGACCTTCGGG 57.371 47.619 0.00 0.00 41.87 5.14
1506 1517 5.879237 TGCTTGATTAATTCGTCAACCATC 58.121 37.500 2.30 0.00 31.55 3.51
1515 1526 4.320690 CGGTGTTGTTGCTTGATTAATTCG 59.679 41.667 0.00 0.00 0.00 3.34
1537 1548 2.800881 TAGCACCTGACATATCTGCG 57.199 50.000 0.00 0.00 30.73 5.18
1549 1560 1.900545 GAGGCCTCCGTTTAGCACCT 61.901 60.000 23.19 0.00 0.00 4.00
1597 1608 1.625315 TCCTTCACCACACTGAGATGG 59.375 52.381 6.06 6.06 42.13 3.51
1687 1698 5.314923 AGCAACAACATTATCACATCACC 57.685 39.130 0.00 0.00 0.00 4.02
1726 1737 8.932945 TCAGAAGTCAGATCATATAACACAAC 57.067 34.615 0.00 0.00 0.00 3.32
1728 1739 7.561356 TCCTCAGAAGTCAGATCATATAACACA 59.439 37.037 0.00 0.00 0.00 3.72
1729 1740 7.865385 GTCCTCAGAAGTCAGATCATATAACAC 59.135 40.741 0.00 0.00 0.00 3.32
1753 1764 8.454106 AGAATGTTTAAGCATCACATAAGTGTC 58.546 33.333 5.19 0.00 46.01 3.67
1801 1818 3.657015 ACACTGATATCATCGGAGCTG 57.343 47.619 5.72 0.00 39.01 4.24
1902 1927 4.949856 ACAACAATTCAACAAGGAGACAGT 59.050 37.500 0.00 0.00 0.00 3.55
1913 1938 3.163630 ACACAGGCACAACAATTCAAC 57.836 42.857 0.00 0.00 0.00 3.18
1935 1960 8.349983 GGTGTGTGTTATAGTTGAACTTTGAAT 58.650 33.333 1.97 0.00 0.00 2.57
1954 1981 3.605634 TCCTAATCCATTTCGGTGTGTG 58.394 45.455 0.00 0.00 35.57 3.82
1972 2005 8.910944 CAACAATTAAATTCTGATGGAGATCCT 58.089 33.333 0.00 0.00 36.82 3.24
1985 2018 8.772705 TGGTTGAATTCTGCAACAATTAAATTC 58.227 29.630 7.05 0.00 45.58 2.17
1999 2032 5.969423 AGGTGCATAAATGGTTGAATTCTG 58.031 37.500 7.05 0.00 0.00 3.02
2021 2054 9.144747 GCAGATCTGTATACAACAACCATATAG 57.855 37.037 23.38 0.00 37.74 1.31
2022 2055 8.646900 TGCAGATCTGTATACAACAACCATATA 58.353 33.333 23.38 0.00 37.74 0.86
2024 2057 6.883744 TGCAGATCTGTATACAACAACCATA 58.116 36.000 23.38 0.00 37.74 2.74
2071 2104 8.709386 ATAAAGAAGTCACTGCATAGTTGTAG 57.291 34.615 0.00 0.00 40.98 2.74
2182 2218 3.120060 CCCTGTCGAAGAAAGCAAAGATG 60.120 47.826 0.00 0.00 41.48 2.90
2183 2219 3.077359 CCCTGTCGAAGAAAGCAAAGAT 58.923 45.455 0.00 0.00 41.48 2.40
2184 2220 2.104111 TCCCTGTCGAAGAAAGCAAAGA 59.896 45.455 0.00 0.00 41.48 2.52
2185 2221 2.481952 CTCCCTGTCGAAGAAAGCAAAG 59.518 50.000 0.00 0.00 41.48 2.77
2186 2222 2.158813 ACTCCCTGTCGAAGAAAGCAAA 60.159 45.455 0.00 0.00 41.48 3.68
2187 2223 1.416401 ACTCCCTGTCGAAGAAAGCAA 59.584 47.619 0.00 0.00 41.48 3.91
2188 2224 1.048601 ACTCCCTGTCGAAGAAAGCA 58.951 50.000 0.00 0.00 41.48 3.91
2189 2225 1.000955 TCACTCCCTGTCGAAGAAAGC 59.999 52.381 0.00 0.00 41.48 3.51
2190 2226 3.386768 TTCACTCCCTGTCGAAGAAAG 57.613 47.619 0.00 0.00 42.75 2.62
2191 2227 3.494398 CCTTTCACTCCCTGTCGAAGAAA 60.494 47.826 0.00 0.00 39.69 2.52
2219 2268 4.084745 GCTTCAGTAGTATCTCGTCTCTCG 60.085 50.000 0.00 0.00 41.41 4.04
2223 2272 4.771903 TCAGCTTCAGTAGTATCTCGTCT 58.228 43.478 0.00 0.00 0.00 4.18
2238 2287 3.256631 ACATTGTTGGAACCATCAGCTTC 59.743 43.478 5.04 0.00 0.00 3.86
2327 2408 7.122353 GCCATAAATTTCCTATCAGATGATGCT 59.878 37.037 5.58 0.00 36.05 3.79
2332 2413 8.415553 TGTTTGCCATAAATTTCCTATCAGATG 58.584 33.333 0.00 0.00 0.00 2.90
2415 3269 6.863126 CACCGCAAGTCAAGATTCTAAAATTT 59.137 34.615 0.00 0.00 0.00 1.82
2423 3277 0.804989 CCCACCGCAAGTCAAGATTC 59.195 55.000 0.00 0.00 0.00 2.52
2442 3296 0.814457 TTGTTGCCCTGTGAACACAC 59.186 50.000 3.39 0.00 36.21 3.82
2585 3439 4.498682 GCATCATGTTGACTTATTCCAGCC 60.499 45.833 7.98 0.00 0.00 4.85
2765 5210 9.716531 AGTACATGATCACATATTAGACCATTG 57.283 33.333 0.00 0.00 35.09 2.82
2770 5215 9.547753 AACCAAGTACATGATCACATATTAGAC 57.452 33.333 0.00 0.00 35.09 2.59
2780 5225 4.759693 GTCACCAAACCAAGTACATGATCA 59.240 41.667 0.00 0.00 0.00 2.92
2781 5226 5.003804 AGTCACCAAACCAAGTACATGATC 58.996 41.667 0.00 0.00 0.00 2.92
2907 8151 7.703298 TGCAGTTTTTCTCAATCATGAAAAG 57.297 32.000 0.00 0.00 41.31 2.27
2977 8226 4.851639 AGAGGAAACTTGCCACTGATAT 57.148 40.909 0.00 0.00 44.43 1.63
2999 8264 9.915629 GGTTATCAGATTCTAGTTACGATTCAT 57.084 33.333 0.00 0.00 0.00 2.57
3000 8265 8.909923 TGGTTATCAGATTCTAGTTACGATTCA 58.090 33.333 0.00 0.00 0.00 2.57
3006 8271 8.008513 TGAGGTGGTTATCAGATTCTAGTTAC 57.991 38.462 0.00 0.00 0.00 2.50
3038 8303 8.383175 ACCATTGTACTGATCCTTTCTAAGAAA 58.617 33.333 0.00 0.00 0.00 2.52
3044 8312 7.016153 TGTAACCATTGTACTGATCCTTTCT 57.984 36.000 0.00 0.00 0.00 2.52
3063 8331 4.572389 CAGCAAGGGATGTGATACTGTAAC 59.428 45.833 0.00 0.00 0.00 2.50
3109 8377 0.462581 ATCTGCATGGTACTGGCACG 60.463 55.000 0.00 0.00 34.76 5.34
3147 8415 4.094294 TGGTACTGCGCTTGTGATAATTTC 59.906 41.667 9.73 0.00 0.00 2.17
3196 8464 2.706890 GAAAGACGGTCCTAATTGCCA 58.293 47.619 4.14 0.00 0.00 4.92
3210 8478 9.393249 TGATTTTGTCAAAATACATCGAAAGAC 57.607 29.630 20.82 7.11 41.49 3.01
3213 8481 9.352784 GGATGATTTTGTCAAAATACATCGAAA 57.647 29.630 29.05 13.46 40.97 3.46
3214 8482 8.739039 AGGATGATTTTGTCAAAATACATCGAA 58.261 29.630 29.05 14.29 40.97 3.71
3216 8484 8.915871 AAGGATGATTTTGTCAAAATACATCG 57.084 30.769 29.05 0.00 40.97 3.84
3235 8503 2.420022 CGGAAAGCCACAGTAAAGGATG 59.580 50.000 0.00 0.00 0.00 3.51
3251 8519 1.469703 CAGCTGATGATGCAACGGAAA 59.530 47.619 8.42 0.00 0.00 3.13
3262 8530 0.388294 CTGCTCGATCCAGCTGATGA 59.612 55.000 17.39 5.01 39.97 2.92
3322 8590 6.096705 TGCTGCCTAATTTATGCTGTATTGTT 59.903 34.615 0.00 0.00 0.00 2.83
3323 8591 5.593909 TGCTGCCTAATTTATGCTGTATTGT 59.406 36.000 0.00 0.00 0.00 2.71
3325 8593 5.593909 TGTGCTGCCTAATTTATGCTGTATT 59.406 36.000 0.00 0.00 0.00 1.89
3393 8661 2.747446 GTTCATTGCCGGTAATGTCAGT 59.253 45.455 34.80 6.57 38.77 3.41
3394 8662 2.746904 TGTTCATTGCCGGTAATGTCAG 59.253 45.455 34.80 17.14 38.77 3.51
3395 8663 2.486203 GTGTTCATTGCCGGTAATGTCA 59.514 45.455 34.80 30.16 38.77 3.58
3416 8684 1.022735 GTGAGGATTCAGCCTGCATG 58.977 55.000 0.00 0.00 38.73 4.06
3427 8695 6.897966 ACATATCCGATAGTATGGTGAGGATT 59.102 38.462 0.00 0.00 37.99 3.01
3476 8744 2.746362 GGGCATGGATGATTTCGATCTC 59.254 50.000 0.00 0.00 0.00 2.75
3481 8749 2.166050 TGTTTGGGCATGGATGATTTCG 59.834 45.455 0.00 0.00 0.00 3.46
3488 8756 1.350071 TTGCTTGTTTGGGCATGGAT 58.650 45.000 0.00 0.00 38.30 3.41
3497 8765 5.401550 TCTGTTCTTCAGTTTGCTTGTTTG 58.598 37.500 0.00 0.00 43.97 2.93
3588 8858 2.107953 GGGAGGAGCACTGATCGC 59.892 66.667 0.00 0.00 0.00 4.58
3594 8864 2.173569 GTGAAATATGGGGAGGAGCACT 59.826 50.000 0.00 0.00 0.00 4.40
3609 8879 4.927267 TCATGTCTAAGGTGGGTGAAAT 57.073 40.909 0.00 0.00 0.00 2.17
3623 8893 2.098280 CGACCTCGATCAGTTCATGTCT 59.902 50.000 0.00 0.00 43.02 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.